After joining Donghak, Son entered into a period of profound training that included reading and reciting the Donghak "Incantation of Twenty-One Letters" thirty thousand times a day. In addition he made straw sandals, which he sold at the market in Cheongju. He is thought to have lived in this manner for roughly three years.

After this period, Son Byong-Hi became the student of Choe Si-hyeong, who was the second leader of Donghak, and entered a life of devoted study. In 1894 Choe Si-hyeong led the Donghak Peasant Revolution in protest at the corruption of the Joseon government, and Son Byong-Hi served as a commander. This revolution quickly grew into a resistance struggle against foreign invasion and occupation, in which Japan was the principal target. Choe's forces met defeat in 1895, however, and the revolution was put down at the hands of Japan's superior modern weaponry. After living for some years as a fugitive, Choe Si-hyeong was captured by pursuing government troops in 1898 and executed, although he had foreseen that his time was marked, and on December 24, 1897 he ordained Son Byong-Hi as the 3rd Great Leader of Donghak.

In 1898, following the execution of Choe Si-hyeong, Son Byong-Hi sought political asylum in Japan. After the Russo-Japanese War in 1904, he returned to Korea and established the Jinbohoe ("progressive society"), a new cultural and reformist movement designed to reverse the declining fortunes of the nation and to create a new society. Through Donghak he conducted a nationwide movement that aimed at social improvement through the renovation of old customs and ways of life. Hundreds of thousands members of Donghak cut their long hair short and initiated the wearing of simple, modest clothing. Non-violent demonstrations for social improvement organised by members of Donghak took place throughout 1904. This coordinated series of activities was known as the Gapjin reform movement.

Members of Donghak were severely persecuted by the Japanese government, and so, on December 1, 1905, Son decided to modernise the religion and usher in an era of openness and transparency in order to legitimise it in the eyes of the Japanese. As a result, he officially changed the name of Dong Hak to Cheondogyo ("Heavenly Way"). The following year, Cheondogyo was established as a modern religious organisation. Its central headquarters were in Seoul.

Over the years of Japanese colonial rule since the annexation in 1910, Son Byong-Hi, like all Koreans, longed for freedom and independence. As a result of these years of oppression, he helped to set up a systematic underground anti-Japanese movement throughout 1918 which saw unprecedented cooperation between Cheondogyo, Christians and Buddhists as they united under a common cause. Son's Cheondogyo gave financial support to the whole movement, and he insisted that the independence movement must be popular in nature and non-violent. A Declaration of Independence was prepared and 33 national leaders selected, 15 of which were members of Cheondogyo. Son Byong-Hi was the most prominent of these.

The climax came on March 1, 1919 when, during a period of public mourning for the recently deceased Emperor Gojong, the Declaration of Independence was publicly proclaimed at Pagoda Park in Seoul—this was known as the March 1st Movement, or Samil Movement. This spark ignited the public, who took to the streets and demonstrated, calling for Korean independence. This initiated a nationwide movement in which many people took part, regardless of locality and social status, but the Japanese immediately mobilised their police and army and brutally put down the demonstrations, despite their peaceful nature. More than 7,500 Koreans were killed, nearly 17,000 wounded, and around 47,000 arrested, including Son Byong-Hi.

While in prison, Son became ill and was eventually released from custody on sick bail. His illness worsened, however, and in 1922 he died at home in Sangchunwon, just outside the Dongdaemun gate.

The Taekwondo pattern Eui-Am was named in honor of Son Byong-Hi after his respectful title of Eui-am Seong-sa.